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Category: Jupyter Notebook

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Hints and Tutorials Jupyter Notebook

Using the Python 3 library FPsim2 for similarity searches

6 April 20236 April 2023 chris

FPsim2 is a new tool for fast similarity search on big compound datasets (>100 million) being developed at ChEMBL. It was developed as a Python3 library

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Download multiple PDB files using a Jupyter notebook

1 April 202322 January 2024 chris

The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists

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Hints and Tutorials Jupyter Notebook

Jupyter Notebook for docking either locally or using Colab

17 February 202317 February 2023 chris

Here are two variations of a Jupyter Notebook to help with docking experiments. The first version runs locally and requires the user to install RDKit,

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  • View post by on Bluesky

    @macinchem.bsky.social 20 hours

    A few upcoming meetings that may be of interest

    Cambridge Cheminformatics Meeting Cambridge Cheminformatics Meeting, 22 April 2026 *** AI Agents for Omics *** Chemical Space Docking for Billion-Sized Libraries...

    https://macinchem.org/2026/04/15/a-few-upcoming-meetings-that-may-be-of-interest/
  • View post by on Bluesky

    @macinchem.bsky.social 2 days

    iNMR updated 7.1.1 released

    iNMR is a fantastic app for NMR spectroscopy, it has been around for over 20 years and gets better with every release. It has been compiled for the Apple...

    https://macinchem.org/2026/04/14/inmr-updated-7-1-1-released/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    Cambridge Cheminformatics Network Meeting

    Cambridge Cheminformatics Meeting, 22 April 2026 *** AI Agents for Omics *** Chemical Space Docking for Billion-Sized Libraries *** Quantum Chemistry for Protein-Ligand...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    mlxmolkit — GPU-accelerated molecular toolkit on Apple Silicon

    I've previously written about mlxmolkit in particular for clustering where see a 40-fold improvement in speed. The toolkit has now...

    https://macinchem.org/2026/04/08/mlxmolkit-gpu-accelerated-molecular-toolkit-on-apple-silicon/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    RSC CICAG Chemical Structure Representations Meeting 2026 

    We do have a lot of different molecular file format, from simple line notations like SMILES to cartesian coordinates (.xyz) to .trexio...

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  • A few upcoming meetings that may be of interest
  • iNMR updated 7.1.1 released
  • Cambridge Cheminformatics Network Meeting
  • mlxmolkit — GPU-accelerated molecular toolkit on Apple Silicon
  • RSC CICAG Chemical Structure Representations Meeting 2026 
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